3N3I

Crystal Structure of G48V/C95F tethered HIV-1 Protease/Saquinavir complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Insights into the mechanism of drug resistance: X-ray structure analysis of G48V/C95F tethered HIV-1 protease dimer/saquinavir complex

Prashar, V.Bihani, S.C.Das, A.Rao, D.R.Hosur, M.V.

(2010) Biochem.Biophys.Res.Commun. 396: 1018-1023

  • DOI: 10.1016/j.bbrc.2010.05.049

  • PubMed Abstract: 
  • The mutation G48V in HIV-1 protease is a major resistance mutation against the drug saquinavir. Recently, G48V mutation is found to co-exist with the mutation C95F in AIDS patients treated with saquinavir. We report here the three-dimensional crystal ...

    The mutation G48V in HIV-1 protease is a major resistance mutation against the drug saquinavir. Recently, G48V mutation is found to co-exist with the mutation C95F in AIDS patients treated with saquinavir. We report here the three-dimensional crystal structure of G48V/C95F tethered HIV-1 protease/saquinavir complex. The structure indicates following as the possible causes of drug resistance: (1) loss of direct van der Waals interactions between saquinavir and enzyme residues PHE-53 and PRO-1081, (2) loss of water-mediated hydrogen bonds between the carbonyl oxygen atoms in saquinavir and amide nitrogen atoms of flap residues 50 and 1050, (3) changes in inter-monomer interactions, which could affect the energetics of domain movements associated with inhibitor-binding, and (4) significant reduction in the stability of the mutant dimer. The present structure also provides a rationale for the clinical observation that the resistance mutations C95F/G48V/V82A occur as a cluster in AIDS patients.


    Organizational Affiliation

    Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A
203Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 4 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ROC
Query on ROC

Download SDF File 
Download CCD File 
A
(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1-phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide
Fortovase; SAQUINAVIR,RO 31-8959
C38 H50 N6 O5
QWAXKHKRTORLEM-UGJKXSETSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000454 (ROC)
Query on PRD_000454
ASaquinavirPeptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ROCIC50: <0.4 nM (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.216 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.410α = 90.00
b = 62.410β = 90.00
c = 83.260γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Type: Other
  • Version 1.3: 2017-08-09
    Type: Source and taxonomy